Biology Reference
In-Depth Information
Biological Petri Nets
Cell Illustrator 4.0: A Computational
Platform for Systems Biology
Masao Nagasaki
∗
, Ayumu Saito, Euna Jeong, Chen Li, Kaname Kojima, Emi Ikeda and
Satoru Miyano
Human Genome Center, Institute of Medical Science, University of Tokyo, Japan
ABSTRACT:
Cell Illustrator is a software platform for Systems Biology that uses the concept of Petri net for modeling and
simulating biopathways. It is intended for biological scientists working at bench. The latest version of Cell Illustrator 4.0
uses Java Web Start technology and is enhanced with new capabilities, including: automatic graph grid layout algorithms
using ontology information; tools using Cell System Markup Language (CSML) 3.0 and Cell System Ontology 3.0; parameter
search module; high-performance simulation module; CSML database management system; conversion from CSML model to
programming languages (FORTRAN, C, C++, Java, Python and Perl); import from SBML, CellML, and BioPAX; and, export to
SVG and HTML. Cell Illustrator employs an extension of hybrid Petri net in an object-oriented style so that biopathway models
can include objects such as DNA sequence, molecular density, 3D localization information, transcription with frame-shift,
translation with codon table, as well as biochemical reactions.
KEYWORDS:
Biopathway, simulation, Petri net, modeling, pathway database, ontology, CSML, CSO, CI, ODE, Cell Illus-
trator, Java, JWS
INTRODUCTION
Systems Biology requires computational tools that enable us to understand and analyze complex
biopathways. A strong need is a biology-oriented software with which biological scientists (users) can
intuitively model and simulate complex dynamic interactions and processes in biopathways comprising
of hundreds of entities within and among cells,
e.g.
, gene regulatory networks, metabolic pathways,
signal transduction pathways, and cell-cell interactions. To this aim, we started developing a software
tool in 1999; the first version was published as Genomic Object Net 1.0 in 2002 [1,2], and it was later
released under the name Cell Illustrator 1.0.
This paper presents the new technologies and tools introduced to the latest version of Cell Illustrator
4.0 while discussing their impacts on biopathway modeling and simulation. For instance, Cell Illustrator
4.0 uses Java Web Start [3] and includes new pathway layout algorithms [4-7], formats
{
Cell System
Markup Language (CSML) [8], Cell System Ontology (CSO) [9]
}
and tools related to pathway modeling
and simulation. Cell Illustrator employs the concept of a hybrid Petri net [10,11] as the modeling method.
We extended this concept for object-oriented style and developed its core architecture, hybrid functional
∗
Corresponding author. Tel.: +81 5449 5615; Fax: +81 5449 5442; E-mail:
masao@ims.u-tokyo.ac.jp
.
